
Hi! I've found that the best size for a whelping box is a square one with enough room for the bitch to lie flat on her side with her head flat too - so the distance from her nose to her tail - with the pigrail at the height of her spine when she's lying flat. Your whelping box sounds fine sizewise.
Can I ask where the bitch rears her pups? Is it in the house or elsewhere? I ask because of the temperature for the pups - if they're too hot they'll be well spread about and maybe more likely to be sat on in the early days. If they're too cool then they'll all be huddled in a heap.
The only other way to avoid squashed puppies is to have someone keeping watch 24/7 (yes, people do this) to physically move any pups that get sat on. I've found that after the first few days bitches become much more adept with their pups and the likelihood of accidents is greatly reduced, to the extent where I remove the pigrails after at the most a week (if only because the pups have grown so much they get stuck underneath them by then!).
Hope this helps.
:)